def test_migrate_all_dbs_with_cherry_picked_samples_mocked(
config, mongo_database, mock_mysql_connection, mock_update_dart
):
_, mongo_db = mongo_database
start_datetime = datetime(year=2020, month=5, day=10, hour=15, minute=10)
end_datetime = start_datetime + timedelta(days=1)
# generate and insert sample rows into the mongo database
test_samples = generate_example_samples(range(0, 6), start_datetime)
mongo_db.samples.insert_many(test_samples)
assert mongo_db.samples.count_documents({}) == 8
cherry_picked_sample = {
FIELD_ROOT_SAMPLE_ID: [test_samples[0][FIELD_ROOT_SAMPLE_ID]],
FIELD_PLATE_BARCODE: [test_samples[0][FIELD_PLATE_BARCODE]],
}
cherry_picked_df = pd.DataFrame.from_dict(cherry_picked_sample)
with patch(
"migrations.helpers.dart_samples_update_helper.get_cherrypicked_samples", side_effect=[cherry_picked_df]
):
with patch(
"migrations.helpers.dart_samples_update_helper.remove_cherrypicked_samples"
) as mock_remove_cherrypicked_samples:
migrate_all_dbs(config, start_datetime.strftime("%y%m%d_%H%M"), end_datetime.strftime("%y%m%d_%H%M"))
samples = get_samples(mongo_db.samples, start_datetime, end_datetime)
mock_remove_cherrypicked_samples.assert_called_once_with(
samples, [[cherry_picked_sample[FIELD_ROOT_SAMPLE_ID][0], cherry_picked_sample[FIELD_PLATE_BARCODE][0]]]
)
def test_migrate_all_dbs_returns_early_failed_mlwh_update(
config, mock_mysql_connection, mock_update_dart):
start_datetime = datetime(year=2020, month=5, day=10, hour=15, minute=10)
end_datetime = start_datetime + timedelta(days=1)
test_samples = generate_example_samples(range(0, 6), start_datetime)
def side_effect(_, collection_name):
mock_collection = MagicMock()
if collection_name == COLLECTION_SAMPLES:
mock_collection.aggregate.return_value = test_samples
elif collection_name == COLLECTION_SOURCE_PLATES:
mock_collection.find_one.return_value = None
else:
raise ValueError(f"{collection_name} is not recognized/expected")
return mock_collection
with patch(
"migrations.helpers.dart_samples_update_helper.get_mongo_collection",
side_effect=side_effect):
mock_mysql_connection.side_effect = Exception(
"Boom!") # mock creating MLWH mysql connection to fail
migrate_all_dbs(config, start_datetime.strftime("%y%m%d_%H%M"),
end_datetime.strftime("%y%m%d_%H%M"))
mock_update_dart.assert_not_called()
def test_migrate_all_dbs_return_early_no_samples(config, mock_mysql_connection,
mock_update_dart):
start_datetime = datetime(year=2020, month=5, day=10, hour=15, minute=10)
end_datetime = start_datetime + timedelta(days=1)
mock_samples_collection = MagicMock()
mock_samples_collection.aggregate.return_value = [
] # mock samples collection call
mock_source_plates_collection = MagicMock()
def side_effect(_, collection_name):
if collection_name == COLLECTION_SAMPLES:
return mock_samples_collection
elif collection_name == COLLECTION_SOURCE_PLATES:
return mock_source_plates_collection
else:
raise ValueError(f"{collection_name} is not recognized/expected")
with patch(
"migrations.helpers.dart_samples_update_helper.get_mongo_collection",
side_effect=side_effect):
migrate_all_dbs(config, start_datetime.strftime("%y%m%d_%H%M"),
end_datetime.strftime("%y%m%d_%H%M"))
# ensure no updates are made
mock_samples_collection.bulk_write.assert_not_called()
mock_source_plates_collection.insert_many.assert_not_called()
mock_mysql_connection.assert_not_called()
mock_update_dart.assert_not_called()
def test_migrate_all_dbs_returns_early_start_datetime_after_end_datetime(
config, mock_mongo_client, mock_mysql_connection, mock_update_dart):
start_datetime = "201017_1200"
end_datetime = "201016_1600"
migrate_all_dbs(config, start_datetime, end_datetime)
# ensure no database connections/updates are made
mock_mongo_client.assert_not_called()
mock_mysql_connection.assert_not_called()
mock_update_dart.assert_not_called()
def run(config: Config, s_start_datetime: str = "", s_end_datetime: str = "") -> None:
print("-" * 80)
print("STARTING LEGACY DART UPDATE")
print(f"Time start: {datetime.now()}")
start = time.time()
dart_samples_update_helper.migrate_all_dbs(config, s_start_datetime, s_end_datetime)
print(f"Time taken: {round(time.time() - start, 2)}s")
print(f"Time finished: {datetime.now()}")
print("=" * 80)
def test_migrate_all_dbs_returns_early_invalid_end_datetime(
config, mock_mongo_client, mock_mysql_connection, mock_update_dart
):
start_datetime = "201016_1600"
end_datetime = "not a real datetime"
with patch("migrations.helpers.dart_samples_update_helper.valid_datetime_string", side_effect=[True, False]):
migrate_all_dbs(config, start_datetime, end_datetime)
# ensure no database connections/updates are made
mock_mongo_client.assert_not_called()
mock_mysql_connection.assert_not_called()
mock_update_dart.assert_not_called()
def test_migrate_all_dbs_remove_cherrypicked_samples(config, mongo_database, mock_update_dart):
_, mongo_db = mongo_database
start_datetime = datetime(year=2020, month=5, day=10, hour=15, minute=10)
end_datetime = start_datetime + timedelta(days=1)
# generate and insert sample rows into the mongo database
test_samples = generate_example_samples(range(0, 6), start_datetime)
mongo_db.samples.insert_many(test_samples)
assert mongo_db.samples.count_documents({}) == 8
with patch(
"migrations.helpers.dart_samples_update_helper.remove_cherrypicked_samples"
) as mock_remove_cherrypicked_samples:
migrate_all_dbs(config, start_datetime.strftime("%y%m%d_%H%M"), end_datetime.strftime("%y%m%d_%H%M"))
mock_remove_cherrypicked_samples.assert_not_called()
